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Simulation of flow processes in hyper-regulated Mediterranean watersheds is critical when examining general water demand and established ecological flows of River Basin Management Plans. Weather dynamics in the Mediterranean zone in recent decades have been characterised by a natural variation of drought cycles. In addition, exacerbated climate change proves that water fluxes must be estimated with more exhaustive models. The aim of this study is to assess the water balance of the Cega-Eresma-Adaja (CEA) watershed, including a detailed assessment of land uses and management practices to quantify agricultural water demand for the time period 2004-2014. We used the Soil and Water Assessment Tool (SWAT), given that it is a widespread tool that involves complex processes of the water cycle on a basin scale, providing information on water dynamics related to land use as a fundamental characteristic for water balance calculation. The Nash-Sutcliffe coefficient efficiency value, the main index of calibration and validation performance, was 0.86 for the Eresma-Adaja River and 0.67 for the Cega River. This presents a good result considering the large-scale watershed studied. Analysing dry hydrological years, we found that the estimation of ecological flows for sub-arid zones needs to consider the shallow aquifer-river relationship. During spring-summer periods, with very low flow, monitoring the shallow aquifer levels ensures a good ecological status. The study reveals that aspects such as crop rotation, soil management and their associated measures in Mediterranean basins are key factors for water resource management during drought periods. These results are expected to serve stakeholders and river basin authorities in conducting better-integrated water management practices in the watershed.